This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Our automated system for low-dose TEM image acquisition, Leginon, has been the corner stone of our Resource for many years. While our goals for automation have now expanded to include the entire reconstruction pipeline, Leginon remains as one of the most critical steps in this pipeline and efforts in this core contribute to and influence all of the others. In addition, almost every collaborative and service project makes use of Leginon and thus all of these projects in turn help drive the development of the system. The overall specific aims of this Core are to add new procedures for automating the initial setup of the microscope, improve the overall data throughput, provide a number of new applications to support tomography, tilt pair, and diffraction imaging, and to build a software development kit to facilitate the development of additional applications by outside groups.